In these post-genome days, a novel technology for detecting a base type in a nucleotide sequence accurately and efficiently at a low cost is demanded. For example, an SNP (single nucleotide polymorphism) is a most frequent polymorphism present at a rate as high as about 0.1% (1 base per 1000 bases) in a human genome, and its involvement in various diseases become to be clarified (such as an SNP of a p53 gene involved in a lung cancer: See, Non-patent document 1), resulting in an increased need of an exact judgement of the presence or absence of the SNP (an SNP typing) for the purpose of a diagnosis or gene therapy.
While there are known methods of the SNP typing such as “a method utilizing a hybridization efficiency”, “a method utilizing an enzyme recognition efficiency”, “a method utilizing an electric technology” and the like, a method utilizing a hybridization efficiency is investigated especially with regard to the application to a DNA microarray (for example, see Patent documents 1-4, Non-patent documents 2 and 3), and an example of the detection of a BRCA1 gene SNP using a DNA microarray is disclosed for example in Non-patent document 4.
However, a conventional DNA microarray employs a procedure in which a target nucleotide sequence is labeled usually with a fluorescence and the target nucleotide sequence hybridized with a capture probe of the microarray is detected using a fluorescent signal as an index, although such a procedure is not limited to the detection of an SNP. Accordingly, the preparation of the target nucleotide sequence employs means such as a PCR amplification using a labeled dNTP, which requires a substantial work, time and expense. Also in the detection of an SNP or the like, a method using a melting point observed in the hybridization of a probe with a target nucleotide is employed as an index generally, and in such a case an precise adjustment of the stringency condition of a hybridization is required for each of the individual target nucleotides, but even with such an adjustment a problematic error in the measurement attributable for example to a mishybridization can not be avoided.
On the other hand, a fluorescence-modified nucleic acid base having a fluorescent molecule bound to the naturally occurring nucleic acid base is also known, and the utilization of a fluorescent probe with altering the fluorescent signal intensity on the basis of the environment of the hybridized partner strand is proposed for example in Non-patent document 5.    Patent document 1: U.S. Pat. No. 5,474,796    Patent document 2: U.S. Pat. No. 5,605,662    Patent document 3: WO95/25116    Patent document 4: WO95/35505 A1    Non-patent document 1: Biros et al., Neoplasma 48(5): 407-11, 2001    Non-patent document 2: Schena, M. et al., Proc. Natl. Acad. Sci., USA 93:10614-10619, 1996    Non-patent document 3: Heller, R. A. et al., Proc. Natl. Acad. Sci., USA. 94:2150-2155, 1997    Non-patent document 4: Hacia J G et al., Nat. Genet. 14:441-447, 1996    Non-patent document 5: Yamane, A., Nucleic Acid Res 30(19): e97, 2002